9CBQ | pdb_00009cbq

Methionine synthase from Thermus thermophilus HB8, Folate demethylation state (Fol-on)

PDB DOI: https://doi.org/10.2210/pdb9CBQ/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-06-19 Released: 2025-07-02
Deposition Author(s): Yamada, K., Mendoza, J., Koutmos, M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free:
0.268 (Depositor), 0.268 (DCC)
R-Value Work:
0.208 (Depositor), 0.217 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Methionine synthase from Thermus thermophilus HB8, Folate demethylation state (Fol-on)

Mendoza, J., Yamada, K., Koutmos, M.

To be published.

Macromolecule Content

Total Structure Weight: 58.51 kDa
Atom Count: 4,030
Modeled Residue Count: 496
Deposited Residue Count: 511
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine synthase	A	511	Thermus thermophilus HB8	Mutation(s): 1 Gene Names: TTHA0618 EC: 2.1.1.13
UniProt
Find proteins for Q5SKM5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKM5 Go to UniProtKB: Q5SKM5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SKM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 (Subject of Investigation/LOI) Query on B12 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NHE Query on NHE Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A]	C [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain G [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]